Alignment: Practical session

#!/bin/bash
 
#move and create directory
cd ~/mda12
mkdir -p mapping
 
# index reference
time bwa index resources/ref/human_g1k_v37.chr20.fasta
time samtools faidx resources/ref/human_g1k_v37.chr20.fasta
 
# align pair 1
time bwa aln -t 1 -l 40 -k 2 resources/ref/human_g1k_v37.chr20.fasta\
 resources/data/test_1.fq >\
 mapping/test_1.sai
 
# align pair 2
time bwa aln -t 1 -l 40 -k 2 resources/ref/human_g1k_v37.chr20.fasta\
 resources/data/test_2.fq >\
 mapping/test_2.sai
 
# merge Paired-End in SAM
time bwa sampe -n 1\
 resources/ref/human_g1k_v37.chr20.fasta mapping/test_1.sai mapping/test_2.sai\
 resources/data/test_1.fq  resources/data/test_2.fq >\
 mapping/test.sam
 
# SAM to BAM conversion
time samtools view -bS mapping/test.sam -o mapping/test.bam
 
# basic stats all reads
time samtools flagstat mapping/test.bam | tee mapping/flagstat_all.txt
 
# sort and index BAM
time samtools sort mapping/test.bam mapping/test_sorted
time samtools index mapping/test_sorted.bam
 
# filter alignment
time samtools view -S -h -F 4 -q 10 mapping/test.sam | grep -v "XA:Z:" > mapping/test_mapped.sam
 
# SAM to BAM conversion
time samtools view -bS mapping/test_mapped.sam -o mapping/test_mapped.bam
 
# basic stats mapped reads
time samtools flagstat mapping/test_mapped.bam | tee mapping/flagstat_mapped.txt
 
# sort and index BAM
time samtools sort mapping/test_mapped.bam mapping/test_mapped_sorted
time samtools index mapping/test_mapped_sorted.bam
 
# bamQC
/home/biouser.23-10-2012/mda12/qualimap/qualimap
 
# IGV
igv